3GJE | pdb_00003gje

Rational development of high-affinity T-cell receptor-like antibodies

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RZF	PDB ENTRY 1RZF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP			VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.95	58.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.057	α = 90
b = 117.057	β = 90
c = 78.801	γ = 90

Symmetry
Space Group	P 43

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 4		2005-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.934	ESRF	ID14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.3	30				44489	44489	428360

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1RZF	2.3	25	44459	2362	99.04	0.22628	0.22243	0.21	0.30231	0.29	RANDOM	44.399

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.98			0.98		-1.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.43
r_dihedral_angle_4_deg	26.367
r_dihedral_angle_3_deg	19.614
r_dihedral_angle_1_deg	12.773
r_scangle_it	4.029
r_scbond_it	2.731
r_mcangle_it	2.054
r_angle_refined_deg	2.034
r_mcbond_it	1.174
r_nbtor_refined	0.308
r_nbd_refined	0.246
r_symmetry_vdw_refined	0.228
r_xyhbond_nbd_refined	0.2
r_symmetry_hbond_refined	0.164
r_chiral_restr	0.142
r_bond_refined_d	0.021
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6442
Nucleic Acid Atoms
Solvent Atoms	371
Heterogen Atoms

Software

Software
Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling